Human vs Coho salmon LastZ results
Human (Homo sapiens, GRCh38) and Coho salmon (Oncorhynchus kisutch, Okis_V2) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl release 101. Human was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.
Configuration parameters
| Parameter | Value |
|---|---|
| Gap open penalty (O) | 400 |
| Gap extend penalty (E) | 30 |
| HSP threshold (K) | 3000 |
| Threshold for gapped extension (L) | 3000 |
| Threshold for alignments between gapped alignment blocks (H) | 2200 |
| Seed and Transition value (T) | 1 |
| Scoring matrix (Q) | Default:
A C G T
91 -114 -31 -123
-114 100 -125 -31
-31 -125 100 -114
-123 -31 -114 91
|
Chunking parameters
| Parameter | Human | Coho salmon |
|---|---|---|
| Chunk size | 30,000,000 | 10,100,000 |
| Overlap | 0 | 100,000 |
| Group set size | 10,100,000 | |
| Masking options |
Statistics over 424,170 alignment blocks
| Genome coverage (bp) | Coding exon coverage (bp) | |
|---|---|---|
| Human |
Uncovered: 3,062,183,740 out of 3,099,750,718 |
Uncovered: 16,314,167 out of 38,571,754 |
| Coho salmon |
Uncovered: 2,311,866,377 out of 2,375,894,934 |
Uncovered: 37,063,588 out of 81,688,917 |
Block size distribution
| Size range | All 424,170 alignment blocks | Blocks grouped in nets | |||
|---|---|---|---|---|---|
| # blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
| 1 bp - 10 bp | 3,542 |
15.8 kb |
|||
| 10 bp - 100 bp | 84,617 |
6.3 Mb |
28,142 |
2.1 Mb |
|
| 100 bp - 1 kb | 332,661 |
67.5 Mb |
146,800 |
43.3 Mb |
|
| 1 kb - 10 kb | 3,341 |
5.2 Mb |
15,861 |
31.0 Mb |
|
| 10 kb - 100 kb | 8 |
217.5 kb |
142 |
2.4 Mb |
|
| 100 kb - 1 Mb | 1 |
100.2 kb |
4 |
483.9 kb |
|